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https://www.readbyqxmd.com/read/28646868/comprehensive-benchmarking-of-markov-chain-monte-carlo-methods-for-dynamical-systems
#1
Benjamin Ballnus, Sabine Hug, Kathrin Hatz, Linus Görlitz, Jan Hasenauer, Fabian J Theis
BACKGROUND: In quantitative biology, mathematical models are used to describe and analyze biological processes. The parameters of these models are usually unknown and need to be estimated from experimental data using statistical methods. In particular, Markov chain Monte Carlo (MCMC) methods have become increasingly popular as they allow for a rigorous analysis of parameter and prediction uncertainties without the need for assuming parameter identifiability or removing non-identifiable parameters...
June 24, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28646305/the-effect-of-hydrodynamic-and-thermodynamic-factors-and-the-addition-of-citric-acid-on-the-precipitation-of-calcium-oxalate-dihydrate
#2
Anamarija Šter, Silvija Šafranko, Katarina Bilić, Berislav Marković, Damir Kralj
This paper reports on the investigation of experimental conditions relevant for spontaneous precipitation of significant amount of pure calcium oxalate dihydrate (COD). For this purpose, the hydrodynamic and thermodynamic parameters, such as mode of agitation, temperature, supersaturation and concentration of additives (citrate ions), have been studied. The results show that in the model systems, without the citrate addition and applied mechanical stirring, calcium oxalate monohydrate (COM) was observed as dominant modification after 20 min of aging, while the magnetic stirring resulted in a formation of a mixture of COM and calcium oxalate trihydrate (COT), regardless of the temperature applied...
June 23, 2017: Urolithiasis
https://www.readbyqxmd.com/read/28645446/cost-effectiveness-analysis-of-two-treatment-strategies-for-chronic-hepatitis-c-before-and-after-access-to-direct-acting-antivirals-in-spain
#3
Juan Turnes, Raquel Domínguez-Hernández, Miguel Ángel Casado
OBJECTIVE: To evaluate the cost-effectiveness of a strategy based on direct-acting antivirals (DAAs) following the marketing of simeprevir and sofosbuvir (post-DAA) versus a pre-direct-acting antiviral strategy (pre-DAA) in patients with chronic hepatitis C, from the perspective of the Spanish National Health System. METHODS: A decision tree combined with a Markov model was used to estimate the direct health costs (€, 2016) and health outcomes (quality-adjusted life years, QALYs) throughout the patient's life, with an annual discount rate of 3%...
June 20, 2017: Gastroenterología y Hepatología
https://www.readbyqxmd.com/read/28645261/genome-wide-analysis-of-udp-glycosyltransferase-super-family-in-brassica-rapa-and-brassica-oleracea-reveals-its-evolutionary-history-and-functional-characterization
#4
Jingyin Yu, Fan Hu, Komivi Dossa, Zhaokai Wang, Tao Ke
BACKGROUND: Glycosyltransferases comprise a highly divergent and polyphyletic multigene family that is involved in widespread modification of plant secondary metabolites in a process called glycosylation. According to conserved domains identified in their amino acid sequences, these glycosyltransferases can be classified into a single UDP-glycosyltransferase (UGT) 1 superfamily. RESULTS: We performed genome-wide comparative analysis of UGT genes to trace evolutionary history in algae, bryophytes, pteridophytes, and angiosperms; then, we further investigated the expansion mechanisms and function characterization of UGT gene families in Brassica rapa and Brassica oleracea...
June 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28643629/faecal-immunochemical-tests-to-triage-patients-with-lower-abdominal-symptoms-for-suspected-colorectal-cancer-referrals-in-primary-care-a-systematic-review-and-cost-effectiveness-analysis
#5
Marie Westwood, Isaac Corro Ramos, Shona Lang, Marianne Luyendijk, Remziye Zaim, Lisa Stirk, Maiwenn Al, Nigel Armstrong, Jos Kleijnen
BACKGROUND: Colorectal cancer (CRC) is the third most common cancer in the UK. Presenting symptoms that can be associated with CRC usually have another explanation. Faecal immunochemical tests (FITs) detect blood that is not visible to the naked eye and may help to select patients who are likely to benefit from further investigation. OBJECTIVES: To assess the effectiveness of FITs [OC-Sensor (Eiken Chemical Co./MAST Diagnostics, Tokyo, Japan), HM-JACKarc (Kyowa Medex/Alpha Laboratories Ltd, Tokyo, Japan), FOB Gold (Sentinel/Sysmex, Sentinel Diagnostics, Milan, Italy), RIDASCREEN Hb or RIDASCREEN Hb/Hp complex (R-Biopharm, Darmstadt, Germany)] for primary care triage of people with low-risk symptoms...
May 2017: Health Technology Assessment: HTA
https://www.readbyqxmd.com/read/28643582/adverse-childhood-circumstances-and-functional-status-throughout-adult-life
#6
James N Laditka, Sarah B Laditka
OBJECTIVE: We studied the association of childhood adversity with adult functional status. METHOD: With data from the Panel Study of Income Dynamics and the 2014 Childhood Retrospective Circumstances Study (1992-2013; N = 6,705; 62,885 person-years), we estimated functional status transition probabilities associated with childhood adversity, with multinomial logistic Markov models adjusted for age, sex, race/ethnicity, and education. Microsimulation then estimated functional status outcomes throughout adulthood for African American, Hispanic, and non-Hispanic White women and men...
June 1, 2017: Journal of Aging and Health
https://www.readbyqxmd.com/read/28643317/-effect-of-metformin-on-colorectal-carcinoma-in-type-2-diabetes-mellitus-patients-a-markov-model-analysis
#7
Tianhong Su, Bing Liao, Yu Dong, Zhenwei Peng, Qian Zhou, Bin Li, Sui Peng, Ning Zhang
OBJECTIVE: To evaluate the colorectal cancer (CRC) prevention effect of metformin in comparison with that of other T2DM medications from a Markov model perspective. METHODS: Literature concerning CRC morbidity of T2DM patients with metformin or other diabetes medications treatment was reviewed in PubMed and Cochrane Library database from September 2010 to December 2016. INCLUSION CRITERIA: (1)enrolled population was adult patients with T2DM but without CRC; (2) any of the parameters applied in our model was reported; (3) randomized clinical trials (RCTs), quasi-randomized trials, prospective or retrospective cohort studies...
June 25, 2017: Zhonghua Wei Chang Wai Ke za Zhi, Chinese Journal of Gastrointestinal Surgery
https://www.readbyqxmd.com/read/28641078/signal-dimensionality-and-the-emergence-of-combinatorial-structure
#8
Hannah Little, Kerem Eryılmaz, Bart de Boer
In language, a small number of meaningless building blocks can be combined into an unlimited set of meaningful utterances. This is known as combinatorial structure. One hypothesis for the initial emergence of combinatorial structure in language is that recombining elements of signals solves the problem of overcrowding in a signal space. Another hypothesis is that iconicity may impede the emergence of combinatorial structure. However, how these two hypotheses relate to each other is not often discussed. In this paper, we explore how signal space dimensionality relates to both overcrowding in the signal space and iconicity...
June 19, 2017: Cognition
https://www.readbyqxmd.com/read/28640385/cost-effectiveness-analysis-of-consolidation-with-brentuximab-vedotin-for-high-risk-hodgkin-lymphoma-after-autologous-stem-cell-transplantation
#9
Lucy Hui, Gottfried von Keudell, Rong Wang, Amer M Zeidan, Steven D Gore, Xiaomei Ma, Amy J Davidoff, Scott F Huntington
BACKGROUND: In a recent randomized, placebo-controlled trial, consolidation treatment with brentuximab vedotin (BV) decreased the risk of Hodgkin lymphoma (HL) progression after autologous stem cell transplantation (ASCT). However, the impact of BV consolidation on overall survival, quality of life, and health care costs remain unclear. METHODS: A Markov decision-analytic model was constructed to measure the costs and clinical outcomes for BV consolidation therapy compared with active surveillance in a cohort of patients aged 33 years who were at risk for HL relapse after ASCT...
June 22, 2017: Cancer
https://www.readbyqxmd.com/read/28640319/observational-constraints-on-particle-acidity-using-measurements-and-modelling-of-particles-and-gases
#10
J G Murphy, P K Gregoire, A G Tevlin, G R Wentworth, R A Ellis, M Z Markovic, T C VandenBoer
In many parts of the world, the implementation of air quality regulations has led to significant decreases in SO2 emissions with minimal impact on NH3 emissions. In Canada and the United States, the molar ratio of NH3 : SO2 emissions has increased dramatically between 1990 and 2014. In many regions of North America, this will lead the molar ratio of NHx : SO4, where NHx is the sum of particle phase NH4(+) and gas phase NH3, and SO4 is the sum of particle phase HSO4(-) and SO4(2-), to exceed 2. A thermodynamic model (E-AIM model II) is used to investigate the sensitivity of particle pH, and the gas-particle partitioning of NHx and inorganic nitrate, to the atmospheric NHx : SO4 ratio...
June 22, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28640287/cost-effectiveness-of-risk-score-stratified-hepatocellular-carcinoma-screening-in-patients-with-cirrhosis
#11
Nicolas Goossens, Amit G Singal, Lindsay Y King, Karin L Andersson, Bryan C Fuchs, Cecilia Besa, Bachir Taouli, Raymond T Chung, Yujin Hoshida
OBJECTIVES: Hepatocellular carcinoma (HCC) surveillance with biannual ultrasound is currently recommended for all patients with cirrhosis. However, clinical implementation of this "one-size-fits-all" approach is challenging as evidenced by its low application rate. We aimed to evaluate the cost-effectiveness of risk-stratified HCC surveillance strategies in patients with cirrhosis. METHODS: A Markov decision-analytic modeling was performed to simulate a cohort of 50-year-old subjects with compensated cirrhosis...
June 22, 2017: Clinical and Translational Gastroenterology
https://www.readbyqxmd.com/read/28638238/a-computational-methodology-to-overcome-the-challenges-associated-with-the-search-for-specific-enzyme-targets-to-develop-drugs-against-leishmania-major
#12
Larissa Catharina, Carlyle Ribeiro Lima, Alexander Franca, Ana Carolina Ramos Guimarães, Marcelo Alves-Ferreira, Pierre Tuffery, Philippe Derreumaux, Nicolas Carels
We present an approach for detecting enzymes that are specific of Leishmania major compared with Homo sapiens and provide targets that may assist research in drug development. This approach is based on traditional techniques of sequence homology comparison by similarity search and Markov modeling; it integrates the characterization of enzymatic functionality, secondary and tertiary protein structures, protein domain architecture, and metabolic environment. From 67 enzymes represented by 42 enzymatic activities classified by AnEnPi (Analogous Enzymes Pipeline) as specific for L major compared with H sapiens, only 40 (23 Enzyme Commission [EC] numbers) could actually be considered as strictly specific of L major and 27 enzymes (19 EC numbers) were disregarded for having ambiguous homologies or analogies with H sapiens...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28637916/model-based-analysis-of-an-outbreak-of-bubonic-plague-in-cairo-in-1801
#13
Xavier Didelot, Lilith K Whittles, Ian Hall
Bubonic plague has caused three deadly pandemics in human history: from the mid-sixth to mid-eighth century, from the mid-fourteenth to the mid-eighteenth century and from the end of the nineteenth until the mid-twentieth century. Between the second and the third pandemics, plague was causing sporadic outbreaks in only a few countries in the Middle East, including Egypt. Little is known about this historical phase of plague, even though it represents the temporal, geographical and phylogenetic transition between the second and third pandemics...
June 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28635362/costs-and-effectiveness-of-fingolimod-versus-alemtuzumab-in-the-treatment-of-highly-active-relapsing-remitting-multiple-sclerosis-in-the-uk-retreatment-discount-and-disutility
#14
Stephen M Montgomery, Jeanette Kusel, Richard Nicholas, Nicholas Adlard
OBJECTIVE: Patients with relapsing-remitting multiple sclerosis (RRMS) treated with disease modifying therapies (DMTs) who continue to experience disease activity may be considered for escalation therapies such as fingolimod or may be considered for alemtuzumab. Previous economic modelling used Markov models; applying one alternative technique, discrete event simulation (DES) modelling, allows retreatment and long-term adverse events (AEs) to be included in the analysis. METHODS: A DES was adapted to model relapse-triggered retreatment with alemtuzumab and the effect of including ongoing quality-adjusted life year (QALY) decrements for AEs that extend beyond previous one year Markov cycles...
June 21, 2017: Journal of Medical Economics
https://www.readbyqxmd.com/read/28634883/a-minimal-continuous-time-markov-pharmacometric-model
#15
Emilie Schindler, Mats O Karlsson
In this work, an alternative model to discrete-time Markov model (DTMM) or standard continuous-time Markov model (CTMM) for analyzing ordered categorical data with Markov properties is presented: the minimal CTMM (mCTMM). Through a CTMM reparameterization and under the assumption that the transition rate between two consecutive states is independent on the state, the Markov property is expressed through a single parameter, the mean equilibration time, and the steady-state probabilities are described by a proportional odds (PO) model...
June 20, 2017: AAPS Journal
https://www.readbyqxmd.com/read/28633604/a-two-stage-approach-to-the-joint-analysis-of-longitudinal-and-survival-data-utilising-the-coxian-phase-type-distribution
#16
Conor Donnelly, Lisa M McFetridge, Adele H Marshall, Hannah J Mitchell
The Coxian phase-type distribution is a special type of Markov model which can be utilised both to uncover underlying stages of a survival process and to make inferences regarding the rates of flow of individuals through these latent stages before an event of interest occurs. Such models can be utilised, for example, to identify individuals who are likely to deteriorate faster through a series of disease states and thus require more aggressive medical intervention. Within this paper, a two-stage approach to the analysis of longitudinal and survival data is presented...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/28632743/in-silico-assessment-of-the-effects-of-quinidine-disopyramide-and-e-4031-on-short-qt-syndrome-variant-1-in-the-human-ventricles
#17
Cunjin Luo, Kuanquan Wang, Henggui Zhang
AIMS: Short QT syndrome (SQTS) is an inherited disorder associated with abnormally abbreviated QT intervals and an increased incidence of atrial and ventricular arrhythmias. SQT1 variant (linked to the rapid delayed rectifier potassium channel current, IKr) of SQTS, results from an inactivation-attenuated, gain-of-function mutation (N588K) in the KCNH2-encoded potassium channels. Pro-arrhythmogenic effects of SQT1 have been well characterized, but less is known about the possible pharmacological antiarrhythmic treatment of SQT1...
2017: PloS One
https://www.readbyqxmd.com/read/28631197/prioritizing-future-research-on-allopurinol-and-febuxostat-for-the-management-of-gout-value-of-information-analysis
#18
Eric Jutkowitz, Fernando Alarid-Escudero, Hyon K Choi, Karen M Kuntz, Hawre Jalal
OBJECTIVES: The aim of this study was to quantify the value of conducting additional research and reducing uncertainty regarding the cost effectiveness of allopurinol and febuxostat for the management of gout. METHODS: We used a previously developed Markov model that evaluated the cost effectiveness of nine urate-lowering strategies: no treatment, allopurinol-only fixed dose (300 mg), allopurinol-only dose escalation (up to 800 mg), febuxostat-only fixed dose (80 mg), febuxostat-only dose escalation (up to 120 mg), allopurinol-febuxostat sequential therapy fixed dose, allopurinol-febuxostat sequential therapy dose escalation, febuxostat-allopurinol sequential therapy fixed dose, and febuxostat-allopurinol sequential therapy dose escalation...
June 19, 2017: PharmacoEconomics
https://www.readbyqxmd.com/read/28630525/a-bayesian-adaptive-design-for-clinical-trials-in-rare-diseases
#19
S Faye Williamson, Peter Jacko, Sofía S Villar, Thomas Jaki
Development of treatments for rare diseases is challenging due to the limited number of patients available for participation. Learning about treatment effectiveness with a view to treat patients in the larger outside population, as in the traditional fixed randomised design, may not be a plausible goal. An alternative goal is to treat the patients within the trial as effectively as possible. Using the framework of finite-horizon Markov decision processes and dynamic programming (DP), a novel randomised response-adaptive design is proposed which maximises the total number of patient successes in the trial and penalises if a minimum number of patients are not recruited to each treatment arm...
September 2017: Computational Statistics & Data Analysis
https://www.readbyqxmd.com/read/28630425/reconstructing-cell-cycle-pseudo-time-series-via-single-cell-transcriptome-data
#20
Zehua Liu, Huazhe Lou, Kaikun Xie, Hao Wang, Ning Chen, Oscar M Aparicio, Michael Q Zhang, Rui Jiang, Ting Chen
Single-cell mRNA sequencing, which permits whole transcriptional profiling of individual cells, has been widely applied to study growth and development of tissues and tumors. Resolving cell cycle for such groups of cells is significant, but may not be adequately achieved by commonly used approaches. Here we develop a traveling salesman problem and hidden Markov model-based computational method named reCAT, to recover cell cycle along time for unsynchronized single-cell transcriptome data. We independently test reCAT for accuracy and reliability using several data sets...
June 19, 2017: Nature Communications
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